114 research outputs found
Large Scale Image Segmentation with Structured Loss based Deep Learning for Connectome Reconstruction
We present a method combining affinity prediction with region agglomeration,
which improves significantly upon the state of the art of neuron segmentation
from electron microscopy (EM) in accuracy and scalability. Our method consists
of a 3D U-NET, trained to predict affinities between voxels, followed by
iterative region agglomeration. We train using a structured loss based on
MALIS, encouraging topologically correct segmentations obtained from affinity
thresholding. Our extension consists of two parts: First, we present a
quasi-linear method to compute the loss gradient, improving over the original
quadratic algorithm. Second, we compute the gradient in two separate passes to
avoid spurious gradient contributions in early training stages. Our predictions
are accurate enough that simple learning-free percentile-based agglomeration
outperforms more involved methods used earlier on inferior predictions. We
present results on three diverse EM datasets, achieving relative improvements
over previous results of 27%, 15%, and 250%. Our findings suggest that a single
method can be applied to both nearly isotropic block-face EM data and
anisotropic serial sectioned EM data. The runtime of our method scales linearly
with the size of the volume and achieves a throughput of about 2.6 seconds per
megavoxel, qualifying our method for the processing of very large datasets
Recursive Training of 2D-3D Convolutional Networks for Neuronal Boundary Detection
Efforts to automate the reconstruction of neural circuits from 3D electron
microscopic (EM) brain images are critical for the field of connectomics. An
important computation for reconstruction is the detection of neuronal
boundaries. Images acquired by serial section EM, a leading 3D EM technique,
are highly anisotropic, with inferior quality along the third dimension. For
such images, the 2D max-pooling convolutional network has set the standard for
performance at boundary detection. Here we achieve a substantial gain in
accuracy through three innovations. Following the trend towards deeper networks
for object recognition, we use a much deeper network than previously employed
for boundary detection. Second, we incorporate 3D as well as 2D filters, to
enable computations that use 3D context. Finally, we adopt a recursively
trained architecture in which a first network generates a preliminary boundary
map that is provided as input along with the original image to a second network
that generates a final boundary map. Backpropagation training is accelerated by
ZNN, a new implementation of 3D convolutional networks that uses multicore CPU
parallelism for speed. Our hybrid 2D-3D architecture could be more generally
applicable to other types of anisotropic 3D images, including video, and our
recursive framework for any image labeling problem
A Fast Learning Algorithm for Image Segmentation with Max-Pooling Convolutional Networks
We present a fast algorithm for training MaxPooling Convolutional Networks to
segment images. This type of network yields record-breaking performance in a
variety of tasks, but is normally trained on a computationally expensive
patch-by-patch basis. Our new method processes each training image in a single
pass, which is vastly more efficient.
We validate the approach in different scenarios and report a 1500-fold
speed-up. In an application to automated steel defect detection and
segmentation, we obtain excellent performance with short training times
Scene Parsing with Multiscale Feature Learning, Purity Trees, and Optimal Covers
Scene parsing, or semantic segmentation, consists in labeling each pixel in
an image with the category of the object it belongs to. It is a challenging
task that involves the simultaneous detection, segmentation and recognition of
all the objects in the image.
The scene parsing method proposed here starts by computing a tree of segments
from a graph of pixel dissimilarities. Simultaneously, a set of dense feature
vectors is computed which encodes regions of multiple sizes centered on each
pixel. The feature extractor is a multiscale convolutional network trained from
raw pixels. The feature vectors associated with the segments covered by each
node in the tree are aggregated and fed to a classifier which produces an
estimate of the distribution of object categories contained in the segment. A
subset of tree nodes that cover the image are then selected so as to maximize
the average "purity" of the class distributions, hence maximizing the overall
likelihood that each segment will contain a single object. The convolutional
network feature extractor is trained end-to-end from raw pixels, alleviating
the need for engineered features. After training, the system is parameter free.
The system yields record accuracies on the Stanford Background Dataset (8
classes), the Sift Flow Dataset (33 classes) and the Barcelona Dataset (170
classes) while being an order of magnitude faster than competing approaches,
producing a 320 \times 240 image labeling in less than 1 second.Comment: 9 pages, 4 figures - Published in 29th International Conference on
Machine Learning (ICML 2012), Jun 2012, Edinburgh, United Kingdo
Promoting Connectivity of Network-Like Structures by Enforcing Region Separation
We propose a novel, connectivity-oriented loss function for training deep
convolutional networks to reconstruct network-like structures, like roads and
irrigation canals, from aerial images. The main idea behind our loss is to
express the connectivity of roads, or canals, in terms of disconnections that
they create between background regions of the image. In simple terms, a gap in
the predicted road causes two background regions, that lie on the opposite
sides of a ground truth road, to touch in prediction. Our loss function is
designed to prevent such unwanted connections between background regions, and
therefore close the gaps in predicted roads. It also prevents predicting false
positive roads and canals by penalizing unwarranted disconnections of
background regions. In order to capture even short, dead-ending road segments,
we evaluate the loss in small image crops. We show, in experiments on two
standard road benchmarks and a new data set of irrigation canals, that convnets
trained with our loss function recover road connectivity so well, that it
suffices to skeletonize their output to produce state of the art maps. A
distinct advantage of our approach is that the loss can be plugged in to any
existing training setup without further modifications
Learning image segmentation and hierarchies by learning ultrametric distances
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Brain and Cognitive Sciences, 2009.Cataloged from PDF version of thesis.Includes bibliographical references (p. 100-105).In this thesis I present new contributions to the fields of neuroscience and computer science. The neuroscientific contribution is a new technique for automatically reconstructing complete neural networks from densely stained 3d electron micrographs of brain tissue. The computer science contribution is a new machine learning method for image segmentation and the development of a new theory for supervised hierarchy learning based on ultrametric distance functions. It is well-known that the connectivity of neural networks in the brain can have a dramatic influence on their computational function . However, our understanding of the complete connectivity of neural circuits has been quite impoverished due to our inability to image all the connections between all the neurons in biological network. Connectomics is an emerging field in neuroscience that aims to revolutionize our understanding of the function of neural circuits by imaging and reconstructing entire neural circuits. In this thesis, I present an automated method for reconstructing neural circuitry from 3d electron micrographs of brain tissue. The cortical column, a basic unit of cortical microcircuitry, will produce a single 3d electron micrograph measuring many 100s terabytes once imaged and contain neurites from well over 100,000 different neurons. It is estimated that tracing the neurites in such a volume by hand would take several thousand human years. Automated circuit tracing methods are thus crucial to the success of connectomics. In computer vision, the circuit reconstruction problem of tracing neurites is known as image segmentation. Segmentation is a grouping problem where image pixels belonging to the same neurite are clustered together. While many algorithms for image segmentation exist, few have parameters that can be optimized using groundtruth data to extract maximum performance on a specialized dataset. In this thesis, I present the first machine learning method to directly minimize an image segmentation error. It is based the theory of ultrametric distances and hierarchical clustering. Image segmentation is posed as the problem of learning and classifying ultrametric distances between image pixels. Ultrametric distances on point set have the special property that(cont.) they correspond exactly to hierarchical clustering of the set. This special property implies hierarchical clustering can be learned by directly learning ultrametric distances. In this thesis, I develop convolutional networks as a machine learning architecture for image processing. I use this powerful pattern recognition architecture with many tens of thousands of free parameters for predicting affinity graphs and detecting object boundaries in images. When trained using ultrametric learning, the convolutional network based algorithm yields an extremely efficient linear-time segmentation algorithm. In this thesis, I develop methods for assessing the quality of image segmentations produced by manual human efforts or by automated computer algorithms. These methods are crucial for comparing the performance of different segmentation methods and is used through out the thesis to demonstrate the quality of the reconstructions generated by the methods in this thesis.by Srinivas C. Turaga.Ph.D
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